Re: periodic boundary condition in XY, hard wall in Z - errors

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Fri Mar 11 2016 - 21:42:23 CST

Maxim,

thanks!

Do you mean "langevin on" or "LangevinPiston on"? I thought "langevin
on" controls temperature. If not, I am confused. I saw a couple of
sample configuration files marked as NVT simulation where langevin is
set to on... Are you saying that for NVT I need to comment it out as
well?

If you meant LangevinPiston, I just commented it out and ran another
job and my simulation doesn't do anything crazy now. I also used exact
measurements for cellbasis vectors.

Olga

On Fri, Mar 11, 2016 at 4:31 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> Olya,
>
> NAMD config script below has "langevin on", so this is NPT. Again, NPT simulations are used to equilibrate pressure, usually to 1 atm, which is also what you have set in your script. Vacuum has 0 atm. I have hard time imagining what langevinPiston should do in such a case.
>
> Here is a useful message on the subject:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/4142.html
>
> Maxim
>
>> On Mar 11, 2016, at 14:57, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>
>> Maxim,
>>
>> thank you for replying. I am trying to figure out MSM right now and
>> see if it makes difference, I'll try setting exact values for
>> cellbasisvectors too.
>>
>> As for the hard wall: I expected to see expansion in the beginning
>> that does not change further, as it happens when I use PBC in 3D. What
>> I saw is oscillating continuous expansion, i.e. a couple of times
>> during simulation the whole box shrinks and then expands more than it
>> did previous time; the change in proportion (elongation in z) is
>> continuous.
>>
>> I ran simulations in NVT today just to see if it helps me keep the
>> size of the box fixed and I still see the change in proportions and
>> increase in Z, actually the whole box becomes much bigger, and
>> proportions change as well, although not as much as it happens when I
>> run NPT.
>>
>> Here is my configuration file for NVT:
>>
>> # Minimization and Equilibration of argon with PBC in XY
>>
>> structure ar.psf
>> coordinates ar.pdb
>> set outputname ar_force_out
>>
>> firsttimestep 0
>>
>> set temperature 310
>>
>> # Input
>> paraTypeCharmm on
>> parameters My_parameters.rtf
>> temperature $temperature
>>
>>
>> # Force-Field Parameters
>> exclude scaled1-4
>> 1-4scaling 1.0
>> cutoff 12.0
>> switching on
>> switchdist 10.0
>> pairlistdist 14.0
>>
>>
>> # Integrator Parameters
>> timestep 2.0
>> rigidBonds none
>> nonbondedFreq 1
>> fullElectFrequency 2
>> stepspercycle 10
>>
>>
>> # Constant Temperature Control
>> langevin on
>> langevinDamping 5
>> langevinTemp $temperature
>> langevinHydrogen off
>>
>>
>> # Periodic Boundary Conditions
>> cellBasisVector1 62.0 0. 0.0
>> cellBasisVector2 0.0 62.0 0.0
>> #cellBasisVector3 0.0 0 0.0
>> cellOrigin 30.0 30.0 32.5
>>
>> wrapAll on
>>
>> margin 30
>>
>> # Constant Pressure Control (variable volume)
>> useGroupPressure no ;# needed for rigidBonds
>> useFlexibleCell no
>> useConstantArea no
>>
>> langevinPiston on
>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>> langevinPistonPeriod 100.0
>> langevinPistonDecay 50.0
>> langevinPistonTemp $temperature
>>
>> tclForces on
>> tclForcesScript my_force.tcl
>>
>> outputName $outputname
>>
>> restartfreq 500
>> dcdfreq 250
>> xstFreq 250
>> outputEnergies 100
>> outputPressure 100
>>
>>
>> minimize 1000
>> run 50000
>>
>> On Fri, Mar 11, 2016 at 3:34 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>>> It is better to set cellbasisvector[1,2] to exact values.
>>> Because you are not using MSM (and you can’t use PME with non-periodic systems), interactions between atoms in the system aren’t right (they are cut off at 12 AA). You should look into MSM first, it should not be that difficult.
>>>
>>> Now, the fact that your simulation crash ~150,000 steps might indicate a problem that emerges due to multiple time-stepping. Try: "stepspercycle 2".
>>>
>>> Finally, what do you expect to get from an NPT simulation with vacuum along z? How do you expect langevinPiston to work in this situation?
>>>
>>>
>>>
>>>> On Mar 10, 2016, at 20:01, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>>>
>>>> Thank you! I will study MSM method.
>>>>
>>>> I have changed the size of cell vectors back to 62, that is the actual
>>>> size rounded up, and I commented out cellBasisVector3. I ran a number
>>>> of simulations today and I keep seeing the same error when I increase
>>>> the number of timesteps. The margin size does seem to make the job run
>>>> longer, at least I don't see any other correlation. My last run quit
>>>> near 150 000 timesteps (I set it up for 500K timesteps).
>>>>
>>>> Apart from that, I see in vmd that my simulation box actually becomes
>>>> longer in Z-direction, it is a cube in the beginning and then the
>>>> proportion changes. I am not sure how to interpret it, but it looks
>>>> like the size in z does not hold, certainly no hard wall. I wonder if
>>>> there is a way to set up the hard wall in a simple way?
>>>>
>>>> Olga
>>>>
>>>>
>>>>
>>>> On Thu, Mar 10, 2016 at 4:58 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>>>>> Olya,
>>>>>
>>>>> If your system size is 60A in x and y, you should use vectors of length 60 as your "cellbasisvector[1,2]". You are currently using 70, which means you have vacuum in x and y directions and this is not what you want. To simulate a system that is non-periodic along Z with NAMD you have to use Multi-level summation method (look for MSM option in NAMD User’s Guide). I believe you have to remove "cellbasisvector3" instead of specifying 0 0 0 but I’m not 100% positive on that.
>>>>>
>>>>> Maxim
>>>>>
>>>>>
>>>>>> On Mar 10, 2016, at 11:21, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>>>>>
>>>>>> My system consists of 200 argon atoms in a box, PBC in X and Y, I
>>>>>> would like hard wall in Z and my goal is to measure
>>>>>> density/concentration. So I think that NPT is reasonable in my case,
>>>>>> is that correct?
>>>>>>
>>>>>> I commented out PME, because I read that it will speed up
>>>>>> calculations, also because, if I understand it correctly, it requires
>>>>>> all three cell basis vectors to be defined.
>>>>>>
>>>>>> linaccel is commented because I defined my own force in a separate
>>>>>> file for the force.
>>>>>>
>>>>>> Here is my configuration file:
>>>>>>
>>>>>> #############################################################
>>>>>> ## JOB DESCRIPTION ##
>>>>>> #############################################################
>>>>>>
>>>>>> # Equilibration of argon atoms with PBC in XY direction
>>>>>>
>>>>>> #############################################################
>>>>>> ## ADJUSTABLE PARAMETERS ##
>>>>>> #############################################################
>>>>>>
>>>>>> structure ar.psf
>>>>>> coordinates ar.pdb
>>>>>>
>>>>>> set temperature 310
>>>>>> set outputname ar_force_out
>>>>>>
>>>>>> firsttimestep 0
>>>>>>
>>>>>>
>>>>>> #############################################################
>>>>>> ## SIMULATION PARAMETERS ##
>>>>>> #############################################################
>>>>>>
>>>>>> # Input
>>>>>> paraTypeCharmm on
>>>>>> parameters My_parameters.rtf
>>>>>> temperature $temperature
>>>>>>
>>>>>>
>>>>>> # Force-Field Parameters
>>>>>> exclude scaled1-4
>>>>>> 1-4scaling 1.0
>>>>>> cutoff 12.0
>>>>>> switching on
>>>>>> switchdist 10.0
>>>>>> pairlistdist 14.0
>>>>>>
>>>>>>
>>>>>> # Integrator Parameters
>>>>>> timestep 2.0 ;# 2fs/step
>>>>>> rigidBonds all ;# needed for 2fs steps
>>>>>> nonbondedFreq 1
>>>>>> fullElectFrequency 2
>>>>>> stepspercycle 10
>>>>>>
>>>>>>
>>>>>> # Constant Temperature Control
>>>>>> langevin on ;# do langevin dynamics
>>>>>> langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
>>>>>> langevinTemp $temperature
>>>>>> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>>>>>>
>>>>>>
>>>>>> # Periodic Boundary Conditions
>>>>>> cellBasisVector1 62.0 0. 0.0
>>>>>> cellBasisVector2 0.0 62.0 0.0
>>>>>> cellBasisVector3 0.0 0 0.0
>>>>>> cellOrigin 30.0 30.0 32.5
>>>>>>
>>>>>> wrapAll on
>>>>>>
>>>>>> margin 10
>>>>>>
>>>>>> # PME (for full-system periodic electrostatics)
>>>>>> #PME yes
>>>>>> #PMEGridSpacing 1.0
>>>>>>
>>>>>>
>>>>>> # Constant Pressure Control (variable volume)
>>>>>> useGroupPressure yes ;# needed for rigidBonds
>>>>>> useFlexibleCell no
>>>>>> useConstantArea no
>>>>>>
>>>>>> langevinPiston on
>>>>>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>>>>>> langevinPistonPeriod 100.0
>>>>>> langevinPistonDecay 50.0
>>>>>> langevinPistonTemp $temperature
>>>>>>
>>>>>> ##################
>>>>>> ###DEFINE FORCES##
>>>>>> ##################
>>>>>>
>>>>>> tclForces on
>>>>>> tclForcesScript my_force.tcl
>>>>>> #set linaccel "30 0 0"
>>>>>>
>>>>>> # Output
>>>>>> outputName $outputname
>>>>>>
>>>>>> restartfreq 500 ;# 500steps = every 1ps
>>>>>> dcdfreq 250
>>>>>> xstFreq 250
>>>>>> outputEnergies 100
>>>>>> outputPressure 100
>>>>>>
>>>>>>
>>>>>> # Minimization
>>>>>> minimize 100
>>>>>> reinitvels $temperature
>>>>>>
>>>>>> run 100000
>>>>>>
>>>>>> Thanks!!
>>>>>>
>>>>>> Olga
>>>>>>
>>>>>> On Thu, Mar 10, 2016 at 2:05 AM, Norman Geist
>>>>>> <norman.geist_at_uni-greifswald.de> wrote:
>>>>>>> We need to see your full input script, since it looks you're doing npt?
>>>>>>>
>>>>>>> Norman Geist
>>>>>>>
>>>>>>>> -----Ursprüngliche Nachricht-----
>>>>>>>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>>>>>>>> Auftrag von Olya Kravchenko
>>>>>>>> Gesendet: Donnerstag, 10. März 2016 04:23
>>>>>>>> An: NAMD <namd-l_at_ks.uiuc.edu>
>>>>>>>> Betreff: namd-l: periodic boundary condition in XY, hard wall in Z - errors
>>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I would like to apply periodic boundary conditions only in X and Y
>>>>>>>> directions. In my config file I used the following entry:
>>>>>>>>
>>>>>>>> # Periodic Boundary Conditions
>>>>>>>> cellBasisVector1 70.0 0. 0.0
>>>>>>>> cellBasisVector2 0.0 70.0 0.0
>>>>>>>> cellBasisVector3 0.0 0 0.0
>>>>>>>> cellOrigin 30.0 30.0 32.5
>>>>>>>>
>>>>>>>> wrapAll on
>>>>>>>> margin 5
>>>>>>>>
>>>>>>>>
>>>>>>>> When I submit the job it runs for a while until I see the following error:
>>>>>>>>
>>>>>>>> WRITING COORDINATES TO DCD FILE ar_force_out.dcd AT STEP 20750
>>>>>>>> FATAL ERROR: Periodic cell has become too small for original patch grid!
>>>>>>>> Possible solutions are to restart from a recent checkpoint,
>>>>>>>> increase margin, or disable useFlexibleCell for liquid simulation.
>>>>>>>>
>>>>>>>> How can I address this error? Is this the right way to set up PBC in 2
>>>>>>>> dimensions?
>>>>>>>>
>>>>>>>> My simulation cell is actually around (~61 ~61 ~62), as measured by
>>>>>>>> minmax. I played with numbers and noticed that my simulation runs
>>>>>>>> longer if I increase both the margin and cell basis vectors.
>>>>>>>>
>>>>>>>> I saw some of the older threads in the archives where the margin was
>>>>>>>> discussed but it's not clear how large should it be. If I want to run
>>>>>>>> my simulation for 500 000 steps, what margin should I set up?
>>>>>>>>
>>>>>>>> Also, when choosing cell basis vector, how much bigger should it be
>>>>>>>> than what is measured by "measure minmax"?
>>>>>>>
>>>>>
>>>
>

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:52 CST